3P2J | pdb_00003p2j

Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3P2J/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-02 Released: 2010-11-17 
• Deposition Author(s): Kumar, A., Singh, A., Yadav, R., Sinha, M., Arora, A., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution

Kumar, A., Singh, A., Yadav, R., Sinha, M., Arora, A., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.27 kDa 
• Atom Count: 1,583 
• Modeled Residue Count: 191 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	191	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  EC: 3.1.1.29
UniProt
Find proteins for A0R3D3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3D3  Go to UniProtKB:  A0R3D3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.909	α = 90
b = 58.943	β = 90
c = 61.854	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Kumar, A., Singh, A., Yadav, R., Sinha, M., Arora, A., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description